Hyperplexed in-situ targeted proteomics via antibody immunodetection (i.e., >15 markers) is changing how we classify cells and tissues. Differently from other high-dimensional single-cell assays (flow cytometry, single-cell RNA sequencing), the human eye is a necessary component in multiple procedural steps: image segmentation, signal thresholding, antibody validation, and iconographic rendering. Established methods complement the human image evaluation, but may carry undisclosed biases in such a new context, therefore we re-evaluate all the steps in hyperplexed proteomics. We found that the human eye can discriminate less than 64 out of 256 gray levels and has limitations in discriminating luminance levels in conventional histology images. Furthermore, only images containing visible signals are selected and eye-guided digital thresholding separates signal from noise. BRAQUE, a hyperplexed proteomic tool, can extract, in a marker-agnostic fashion, granular information from markers which have a very low signal-to-noise ratio and therefore are not visualized by traditional visual rendering. By analyzing a public human lymph node dataset, we also found unpredicted staining results by validated antibodies, which highlight the need to upgrade the definition of antibody specificity in hyperplexed immunostaining. Spatially hyperplexed methods upgrade and supplant traditional image-based analysis of tissue immunostaining, beyond the human eye contribution.

Palmer amaranth (Amaranthus palmeri S. Watson), a dioecious wind-pollinated plant, is one of the most troublesome crop weeds in the United States and is spreading northward. The prodigious production of seed contributes to establishment of populations and spread across the landscape. Sexual reproduction via outcrossing is likely the primary mode of seed production for this dioecious plant. However, A. palmeri may also be capable of autonomous asexual seed production (apomixis), which could be beneficial during colonization. We conducted two studies of female isolation from pollen to investigate the propensity for autonomous seed production in 19 populations across eastern North America. In the first, we observed low-frequency seed production on many isolated females. Using flow cytometry of seed samples (FCSS) we primarily found patterns of ploidy consistent with sexual reproduction; no significant differences in ploidy between seeds produced on isolated females (putative apomicts) and non-isolated females (putatively sexual) were detected. We also investigated patterns of DNA content and found no evidence in 153 samples for polyploidy, which is often observed in apomictic species. The second female isolation trial utilized sex-specific molecular markers to identify and remove males before flowering, and we observed zero seed production. Overall, we did not detect evidence in support of apomixis in these populations of A. palmeri, suggesting that apomixis is unlikely to have played a role in the northward advance of this species in eastern North America. We also investigated whether there is variation between females and males in size and secondary reproductive traits. We found evidence for sexual dimorphism in three of six traits investigated: females are taller at senescence and produce longer secondary branches and more axillary flowers than males. Differences in cost of reproduction and strategies for pollen release versus pollen capture are likely factors shaping the evolution of sexual dimorphism in this wind-pollinated dioecious plant.

Discarding the first ejaculate is recommended as an alternative for improving seminal quality after long sexual resting, especially when semen should be used for cryopreservation. However, when the males are not in sexual resting the necessity to discarding the first ejaculate is still unknown. Therefore, this study aimed to compare by flow cytometry the quality of the first and second ejaculates. Ten kids and uniform goats between 5 and 6 months of age were used in a completely randomized design. Semen collection was carried out every 4 days, until a total of five ejaculates per animal in each treatment was completed. The fresh and frozen semen collected were processed and analyzed using macroscopic and microscopic parameters, resistance test, hypo-osmotic medium test, and flow cytometry (FC). The FC parameters were production of reactive oxygen species, plasma and acrosomal membrane integrity, and lipid peroxidation of the plasma membrane. The ejaculates did not differ for the resistance test, the reactivity in the hypo-osmotic medium and for the macroscopic and microscopic seminal parameters, except for sperm volume and concentration. The first ejaculate had a higher percentage of minor and total defects. None of the FC parameters analyzed differed between the first and second ejaculates. The first and second ejaculates demonstrated similar seminal qualities, so for Alpine kid goats without a sexual resting period, discarding the first ejaculate it is not recommended.

The dating of pollen grains is emerging as the method of choice for lacustrine climate archives that contain few datable macrofossils. Due to the need for high-purity pollen concentrates, new methods are constantly being developed to precisely separate pollen grains. Flow cytometry represents a promising alternative to conventional approaches, enabling the identification of pollen grains through fluorescence and rapid separation for radiocarbon analysis using accelerator mass spectrometry, which has so far been limited to sediments with a high proportion of conifer pollen. We present a revised method for processing large sediment samples, resulting in high-purity pollen and spore concentrates. Using this approach small- to medium-sized pollen and bryophyte spores were isolated from Lake Van sediment samples (Eastern Anatolia, Turkey) in sufficient purity for radiocarbon dating. However, a systematic age discrepancy between pollen and bryophyte spore concentrates was noted. By adapting the chemical and cytometric methods, pure pollen concentrates can be created for sediments with low organic content enabling age determination of climate archives with a low proportion of large pollen or low pollen concentration.

Flow cytometry analysis emerges as an alternative methodology to microscopy for determination of the Leishmania-infection rates of macrophages. Various flow cytometric approaches have been established for the quantification of Leishmania parasites within host cells, labelled either directly fluorescent dyes or indirectly with fluorescently conjugated antibodies. Although these techniques allow accurate quantification of infection, they fail at detection of non-infected macrophages specifically. This study introduces a new flow cytometric approach for the determination of infection rates of macrophages infected by Leishmania infantum parasites. Prior to infection, J774A.1 macrophages and L. infantum promastigotes were stained separately with PKH26 and PKH67 dyes, respectively. Dual staining enabled detection of each cell type, where non-infected macrophages were also recorded for the quantification. Dual-PKH staining achieved high success in selective staining of promastigotes (99.71%) and macrophages (99.57%). The percentages of parasite-infected macrophages were determined for initial 1:2.5 and 1:10 infection ratios as 15.68 and 61.70%, respectively; indicating significant increase in infection rate parallel to the initial treatment ratio. These results demonstrated that the introduced dual-fluorescence flow cytometric approach can be successfully used as an accurate and rapid quantification method for L. infantum-infected macrophages and strengthens the hypothesis that flow cytometric approaches could replace conventional microscopic methodologies.

The soil-transmitted helminth Ascaris lumbricoides infects ~800 million people worldwide. Some people are heavily infected, harbouring many worms, whereas others are only lightly infected. The mechanisms behind this difference are unknown. We used a mouse model of hepatic resistance to Ascaris, with C57BL/6J mice as a model for heavy infection and CBA/Ca mice as a model for light infection. The mice were infected with the porcine ascarid, Ascaris suum or the human ascarid, A. lumbricoides and immune cells in their livers and spleens were enumerated using flow cytometry. Compared to uninfected C57BL/6J mice, uninfected CBA/Ca mice had higher splenic CD4+ and γδ T cell counts and lower hepatic eosinophil, Kupffer cell and B cell counts. Infection with A. suum led to expansions of eosinophils, Kupffer cells, monocytes and dendritic cells in the livers of both mouse strains and depletions of hepatic natural killer (NK) cells in CBA/Ca mice only. Infection with A. lumbricoides led to expansions of hepatic eosinophils, monocytes and dendritic cells and depletions of CD8+, αβ, NK and NK T cells in CBA/Ca mice, but not in C57BL/6J mice where only monocytes expanded. Thus, susceptibility and resistance to Ascaris infection are governed, in part, by the hepatic immune system.

The experiment described in this research communication aimed to compare the immunological traits of Simmental (sire) × Holstein (dam) crossbred cows with the two parental breeds in the peripartum and early lactation period and to estimate the effects of heterosis for these traits. Flow cytometric evaluation of leukocyte subpopulations was assessed in 16 Crossbred (CR), 8 Holstein (HO) and 8 Simmental (SI) cows. Estimated average values of innate and adaptive immune cells showed statistically significant differences between the crossbred cows and parental breeds. Interestingly, the most relevant differences between the three groups related to adaptive immune cells. In particular, the CR cows showed a lower percentage of CD3+ T lymphocytes compared with the SI group (P < 0.0001) and the highest proportions of CD21+ B lymphocytes among the three groups (P < 0.0001). Furthermore, we found the highest positive value of heterosis for the CD21+ B lymphocytes (7.0) and the lowest negative value for CD3+ T lymphocytes (−4.8) in F1 derived population. It seems reasonable to believe that these differences could affect immune function of crossbred cows.

Ram spermatozoa are very sensitive to any cold shock or oxidative damage, therefore making them unsuitable for prolonged storage or distant transport to specialized laboratories for flow-cytometric analysis. The aim of this study was to stain ram semen samples with several fluorescent markers and analyse their stability during formaldehyde fixation. Briefly, freshly collected semen samples were stained for apoptosis (annexin V-FITC, YO-PRO™-1 and FLICA), acrosomal damage (PNA-AF488 and FITC-conjugated antibody against GAPDHS), mitochondrial activity (Mitotracker probes), oxidative damage [dihydroethidium (DHE) and CellROX™ Green] and cell viability (live/dead fixable viability dyes). Next, samples were fixed in buffer containing formaldehyde and then washed. Stained sample were analyzed using flow cytometer before fixation, immediately after fixation, and at 5 h and 20 h post-fixation. Fluorescent signals and the proportion of positively stained spermatozoa were compared statistically in fresh and post-fixed samples. All examined markers, except YO-PRO-1 (decreased significantly, P < 0.05), retained their fluorescence intensities after fixation. In conclusion, several tested markers were able to withstand formaldehyde fixation of ram semen samples as follows: annexin V and FLICA for apoptosis; PNA for acrosomal status; MitoTracker Red CMXRos for mitochondrial activity; and CellROX Green for oxidative status in combination with a suitable live/dead fixable viability dye. This optimized methodology could help to comprehensively analyse the quality of ram semen from local farms countrywide.

The aim of this study was to evaluate different post-shock temperatures for tetraploid induction in the yellowtail tetra Astyanax altiparanae. Newly fertilized eggs were divided into four groups, three were submitted to heat shock (40°C for 2 min) at 24 min post-fertilization (mpf) and another group remained without shock (control). Groups submitted to temperature shock were further separated at the following temperatures: 22°C, 26°C and 28°C. Survival among embryonic development was counted and at hatching the ploidy was analyzed by flow cytometry. The results showed that the post-shock temperature affects the parameters analyzed and, therefore, must be considered for optimization of the production of tetraploid in A. altiparanae. Those data are innovative and could be used in future studies of basic biology in this species.

Free-living amoeba of the genus Acanthamoeba are ubiquitous protozoa involved in opportunistic and non-opportunistic infection in humans, such as granulomatous amoebic encephalitis and amoebic keratitis. Both infections have challenging characteristics such as the formation of the resistant cysts in infected tissues, hampering the treatment and most usual diagnosis depending on time-consuming and/or low sensitivity techniques. The use of monoclonal antibodies presents itself as an opportunity for the development of more effective alternative diagnostic methods, as well as an important and useful tool in the search for new therapeutic targets. This study investigated the possibility of using a previously produced monoclonal antibody (mAb3), as a diagnostic tool for the detection of Acanthamoeba trophozoites by direct and indirect flow cytometry and immunofluorescence. Immunoprecipitation assay and mass spectrometry allowed the isolation of the antibody's target and suggested it is a transporter part of the CPA (cation: proton antiporter) superfamily. In vitro tests indicate an important role of this target in Acanthamoeba's encystment physiology. Our results support the importance of studying the role of CPA2 transporters in the context of acanthamoebiasis, as this may be a way to identify new therapeutic candidates.

Cytological understanding is an important parameter to understand the genetic architecture of yam bean. The ploidy level and genome size of two cultivated species of yam bean (Pachyrhizus erosus and P. tuberosus) were estimated using flow cytometric analysis of young leaf tissue, with propidium iodide as a fluorescent dye. Six genotypes of P. erosus and three genotypes of P. tuberosus were analysed. Rice (Oryza sativa cv. Nipponbare) and Mung bean (Vigna radiata cv Berken) were used as internal reference standards. Variation of 2C nuclear DNA content among the six P. erousus lines was 4.18%, ranging from 1.17 to 1.22 pg, whereas only 1.8% variation was observed among the three P. tuberosus lines, which ranged from 1.07 to 1.09 pg. Moreover, it was found that the nuclear DNA content of P. tuberosus was lower than that of P. erosus. The result of the flow cytometric analysis showed that all the species were diploid (2n = 2x) and coefficient of variation (CV%) of all the accessions of the two species was less than 3.5%. This is the first report of ploidy analysis and genome size estimation of the leguminous underutilized tuber crop yam bean using flow cytometry. This result will be helpful for yam bean genome sequencing and crop improvement programmes.

Chicken primordial germ cells (PGCs) are the primary pluripotent stem cell types that will differentiate towards germ cells. High aldehyde dehydrogenase (ALDH) activity is considered as a functional marker for the detection of cell ‘stemness’. In our study the ALDEFLUOR™ kit was used for determination of ALDH activity in PGCs. PGCs were co-stained with diethylaminobenzaldehyde (DEAB) and ALDH and analyzed by flow cytometry. Our results showed a small cell population (8.0 ± 3.3%) upon preincubation of the cells with the specific inhibitor DEAB, however cells without inhibitor staining showed a fluorescence shift as an ALDH-positive population (70.5 ± 1.6%). These findings indicate higher expression of ALDH in PGCs and ALDH activity can therefore be used as a new functional marker for the detection of cell ‘stemness’ in chicken PGCs. These results may have importance for characterization of PGCs as a potential genetic resource in poultry. Further research is necessary to elucidate the role of this functional marker in these cells.

Documenting leads and lags in terrestrial records of past climate change is critical to understanding the behavior of Earth’s natural climate system and making reliable predictions of future climate conditions. However, uncertainties of several hundred years in age models make it difficult to distinguish synchronicity and feedbacks in paleo archives. In lakes this is often due to the lack of terrestrial macrofossils in climate-sensitive locations, such as high alpine or dryland settings. The potential of radiocarbon (14C) dating of pollen has long been recognized, but the difficulty of cleanly separating pollen from other kinds of organic carbon has limited its usefulness. Here we report 14C ages on pollen separated by flow cytometry, from a set of closely spaced samples from Mono Lake, California. The accuracy of the pollen ages is tested using well-dated bracketing tephras, the South Mono and North Mono-Inyo tephras. In spite of the purity of the sorted samples, the pollen dates are older than the bounding tephras by ~400 yr, similar to some other pollen-dating studies. While improvements in sample preparation protocols are planned, understanding the geological processes involved in the production, preservation, and deposition of pollen at each site will be critical to developing robust high-resolution age models.

The aim of this study was to optimize protocols for electroporation (EP) and polyfection (PLF) using polyethyleneimine (PEI) for pig sperm transfection and to determine which method was the most efficient. For EP standardization, different voltages, amounts and times of electric pulses were tested using propidium iodide (PI) as reporter. For PLF standardization, different concentrations of fluorescein isothiocyanate (FITC)-labelled PEI (PEI/FITC) were incubated with sperm for different periods of time. Flow cytometry was performed to evaluate the best protocol in terms of cell viability, including cytoplasmic membrane, acrosome, chromatin integrities and mitochondrial potential using the FITC probe, PI, acridine orange (AO) and JC1. Transfections with the plasmid pmhyGENIE-5 were carried out under optimum conditions for each procedure (EP: 500 volts, 500 μs and two pulses; PLF: PEI 0.5 mg/ml and incubation time 10 min). Transfection efficacy was assessed by fluorescence in situ hybridization (FISH). A lower transfection rate was observed for sperm in the control group (17.8%) compared with EP (36.7%), with PLF (76.8%) being the most efficient. These results suggest that the EP and PEI could be an efficient and low cost transfection method for swine sperm. Notably, treated cells showed higher plasmatic the membrane damage (PMD) and/or acrosome damage (AD) indexes, therefore the combination of this procedure with biotechniques that facilitate fecundation (i.e. in vitro fertilization or intracytoplasmic sperm injection) or even inclusion of antioxidant or anti-apoptotic drugs to improve spermatozoa viability would be important.

Genetic selection and nutrition management have played a central role in the development of commercial rabbitry industry over the last few decades, being able to affect productive and immunological traits of the animals. However, the implication of different energy sources in animals from diverse genetic lines achieving such evolutionary success remains still unknown. Therefore, in this work, 203 female rabbits housed and bred in the same conditions were used from their first artificial insemination until their fifth weaning. The animals belonged to three different genetic types diverging greatly on breeding goals (H line, hyper-prolific (n=66); LP line, robust (n=67) and R line, selected for growth rate (n=67), and were assigned to two experimental diets, promoting major differences in energy source (cereal starch or animal fat)). The aims of this work were to: (1) characterize and describe blood leucocyte populations of three lines of rabbit does in different physiological stages during their reproductive period: first artificial insemination, first weaning, second parturition and fifth weaning; and (2) study the possible influence of two different experimental diets on the leucocyte populations in peripheral blood. Flow cytometry analyses were performed on blood samples taken from females at each different sampling stade. Lymphocyte populations at both weanings were characterized by significantly lower counts of total, CD5+ and CD8+ lymphocytes (–19.8, –21.7 and –44.6%; P<0.05), and higher counts of monocytes and granulocytes (+49.2 and +26.2%; P<0.05) than in the other stages. Females had higher blood counts of lymphocytes B, CD8+ and CD25+ and lower counts of CD4+ at first than at fifth weaning (+55.6, +85.8, +57.5, –14.5%; P<0.05). G/L ratio was higher at both weanings (P<0.05), and CD4+/CD8+ ratio increased progressively from the 1AI to the 5 W (P<0.001). Regarding the effect of genetic type in blood leucocyte counts, LP animals presented the highest counts for total, B, CD5+ and CD8+ lymphocytes (+16.7, +31.8, +24.5 and +38.7; P<0.05), but R rabbits showed the highest counts for monocytes and granulocytes (+25.3 and +27.6; P<0.05). The type of diet given during the reproductive life did not affect the leucocyte population counts. These results indicate that there are detectable variations in the leucocyte profile depending on the reproductive stage of the animal (parturition, weaning or none of them). Moreover, foundation for reproductive longevity criteria allows animals to be more capable of adapting to the challenges of the reproductive cycle from an immunological viewpoint.

Within recent years, there has been growing interest in the prediction of bull fertility through in vitro assessment of semen quality. A model for fertility prediction based on early evaluation of semen quality parameters, to exclude sires with potentially low fertility from breeding programs, would therefore be useful. The aim of the present study was to identify the most suitable parameters that would provide reliable prediction of fertility. Frozen semen from 18 Italian Holstein-Friesian proven bulls was analyzed using computer-assisted semen analysis (CASA) (motility and kinetic parameters) and flow cytometry (FCM) (viability, acrosomal integrity, mitochondrial function, lipid peroxidation, plasma membrane stability and DNA integrity). Bulls were divided into two groups (low and high fertility) based on the estimated relative conception rate (ERCR). Significant differences were found between fertility groups for total motility, active cells, straightness, linearity, viability and percentage of DNA fragmented sperm. Correlations were observed between ERCR and some kinetic parameters, and membrane instability and some DNA integrity indicators. In order to define a model with high relation between semen quality parameters and ERCR, backward stepwise multiple regression analysis was applied. Thus, we obtained a prediction model that explained almost half (R2=0.47, P<0.05) of the variation in the conception rate and included nine variables: five kinetic parameters measured by CASA (total motility, active cells, beat cross frequency, curvilinear velocity and amplitude of lateral head displacement) and four parameters related to DNA integrity evaluated by FCM (degree of chromatin structure abnormality Alpha-T, extent of chromatin structure abnormality (Alpha-T standard deviation), percentage of DNA fragmented sperm and percentage of sperm with high green fluorescence representative of immature cells). A significant relationship (R2=0.84, P<0.05) was observed between real and predicted fertility. Once the accuracy of fertility prediction has been confirmed, the model developed in the present study could be used by artificial insemination centers for bull selection or for elimination of poor fertility ejaculates.